I have hard refreshed and even closed the tab and opened a new one for a clean load and it is still doing it constantly and if it isn't then the progress bar is completely absent as in @masonwheeler's case.

So... public/src/modules/navigator.js...When you click on a topic link, navigator.update is called multiple times. But before the last time (why multiple times? no clue) navigator.disable is being called for some reason.

This nulls out navigator.selector, which is the thing with all the data and stuff for where you are on the page, so that makes sense why topic last read markers don't get updated.